During one of their trips, the Doctor and Clara find themselves in Samaritan's stronghold. After being forced to leave Clara behind, the Doctor turns to Team Machine for help in saving her. Doctor Who: pre-series 9 Person of Interest: 2 months after the season 4 season finale

Head Notes: It has been a while since I have been able to post anything. I wanted to write a story that predicted what would happen next in regards to the Machine and Samaritan. But since I already know that anything I write will most likely be disproved, I decided to just have fun with it. So I decided to do a crossover with Doctor Who. Also I want apologize to all those who are following my Monk story. I have officially hit writer's block for that one so it is on hiatus until I figure out what to do with it next.

Enemy of my enemy

Chapter one

"So where are we off to this time?" Clara asked, her eyes flashing in anticipation of their next adventure.

"Well, there's Trighton, the civilization completely built underwater, or we could visit the planet of the Cribbon race. They use their telepathic field to predict and anticipate the needs of any individual. Which comes in very handy for their very own planet-owned restaurant famous throughout the galaxy. Best restaurant in the universe, hands down."

"Well then who am I to miss out on the best restaurant in the universe?" Clara decided.

"I thought you would say that." The Doctor stated, grinning as he threw the gears into place.

The TARDIS's melodious atmosphere flashed and groaned happily. Clara had had no idea how much she had come to love that sound until she'd spent time without it. It had only been a few weeks between the time Danny died and when the Doctor came back for her but those few weeks with no distraction, no time and space adventures, and no excitement outside of teaching had nearly driven her mad. And to think she had almost lost it.

When Danny had died so suddenly, she'd been so desperate to save him, so impulsive that she had taken her anger and confusion out on the Doctor. The only two men that had ever served any real purpose in her life, and in her rash judgement she had nearly lost them both. The TARDIS groaned as its gears wound down, landing with a thud.

"What's the weather like there?" Clara wondered. "Is it hot, warm, or cold?"

"It's fine," The Doctor insisted, opening the doors.

The sight that met him outside the TARDIS stopped him in his tracks. A windowless room crowded with servers and a variety of computer equipment. The sliding door on the other side of the room with an electronic lock however, told him that this wasn't a normal server room. He didn't know where he was but it wasn't at the restaurant. He doubted that they had even left Earth.

"What's going on, Doctor?" He heard behind him as Clara followed him out of the TARDIS. "This isn't the restaurant, is it?"

"Ah! You noticed that, did you" He stated sarcastically. "Yes, I think it's a fair assumption to say we missed the restaurant. I don't think we've even left Earth.

"Where are we?" She asked.

"Geographically," the doctor began, moving around the room. "Somewhere in North America. Possibly the East Coast. Specifically, I have no idea."

He took out the Sonic Screwdriver and scanned around the room. "We are in some kind of server room."

"What?"

"Where businesses store their computer systems," he explained.

"Okay, Doctor, that's all fine and everything, but can we not just go?" Clara nagged. "We did agree to go to the restaurant."

"We can't. Not until I've figured out what this is," he insisted, continuing to scan the room.

"You just said that this was a server room," Clara reminded him impatiently.

"It's not a normal server room," he hushed. "I don't know what it is but there's something different about it. Like it's linked to something bigger."

"Like what?" Clara wondered.

"I don't know," he breathed. "But one thing's for certain. We are never going to find out by staying in here." He said as he held the sonic to the electronic lock.

The door slid open and the Doctor and Clara stepped out into the cool hallway.

"So, what do we look for?" Clara asked.

"Anomalies," he answered. "Anything that sets this place apart from any other."

Neither of them noticed or cared that there was a security camera overlooking the entire hallway. Even if they had, neither of them would know that the camera's observations were being directly uploaded into the brain of an Artificial Intelligence. Including the observation of two unidentified intruders roaming the halls where no unauthorized persons were allowed. The two intruders silently moved down the hall unaware of the danger they were in.

The Doctor suddenly stopped in his tracks.

"What is it?" Clara whispered.

"Shush!" He hissed.

He raised the sonic screwdriver into the air. Just as he thought. There was a stream of silent communication being broadcasted throughout the building. He couldn't hear what they were saying, but he didn't like their chances.

"I think we might have company," he whispered to Clara.

No sooner had he said those words that alarms in the building began blaring loud and sharp in their ears. The Doctor and Clara instinctively covered their ears at the sudden racket.

"Run," the Doctor ordered, turning back toward the room they had left.

His side burned as he bolted down the hall. He heard Clara behind him, panting to keep up with him. Just then he heard a gunshot and a bullet whistled past his ear. Of course, what else could it be? He raised the sonic as he drew nearer to the door in front of the TARDIS and the locks disengaged, sliding the door open. Just as he got to it, it started to slide close again. With a desperate leap of energy he dove through the door just before it slammed shut.

"Doctor!" Clara called after him, and desperately pounding on the door.

"Hold on!" he called, sonicing the door. The door opened only halfway before forcing its way closed again. "No! No!" He boosted the sonic but it only slowed the door.

He looked past the crack in the door to Clara's panicked eyes.

"I'm sorry," he said. "I can't open the door. Some very strong technology is interfering with it."

Clara looked behind her and back at him. "Then go." She insisted, the fear in her eyes palpable. "They'll be here any second."

"They will kill you," he stated.

"I very much doubt it," she said.

"Why?"

"Because, my friend will not rest until he finds a way to save me in the nick of time," she said, smiling through her fear. "Now go."

The Doctor gave one last look at Clara.

"I will find a way to save you." He said even though he was sure there was no way.

He released the sonic and the door clamped shut.

XxXxXxX

Clara looked after the doctor as long as she could before the door finally closed. She knew there was no way out for her. As soon as the men with the guns found her she was as good as dead. But the look in the Doctor's eyes was already painful. She gave him hope that he might be able to save her, because that was the only way she'd get him to leave. Sure enough, a few moments later she heard the TARDIS powering up and the sound faded just a few seconds later. Just as the stampede of feet rounded the corner to where she was.

She turned to face them, determined to remain defiant to the end. They were going to kill her anyway. She might as well go out with a bit of dignity intact. At least a dozen people, men and women, surrounded her pointing high-powered firearms at her.

"Now, now, let's all calm down," an older gentleman said in a British Accent, making his way through the crowd. "Now young lady, where has your friend gone to?"

XxXxXxX

Harold Finch fumbled with the briefcase again. Working desperately in the underground subway base, he had managed to give the newborn Machine new capabilities but he wouldn't be able to see the full result until he switched it on, at which point Samaritan would detect it. He and Root had tried small test runs. Root had likened it to giving a child permission to walk around the block. At first it couldn't do much more than observe. But with each test run, they ran different simulations of the different functions. Testing out its abilities one at a time. Today they would expand its horizons. They were going to test its ability to see and act on information it perceived. Dangerous, but necessary to let it grow any further.

"Are we ready?" He asked, turning stiffly to her.

"Time to resurrect god," she whispered seductively.

Harold flicked the switch and the lights flickered to life. Root closed her eyes as the information the Machine processed coursed through the Cochlear implant into her mind.

"What does it see?" he asked.

"Give her a minute, She has to sort through it all," she hushed. "Hold on, She's seeing something. Someone."

"There are 7 billion people in the world," Harold pointed out.

"She says there is something different about this man," she reported. "I'd almost say She was excited to see him. Like She can't wait to meet him."

Harold narrowed his eyes, puzzled. "Who?"

"Excuse me, Harold," she pardoned. "She wants me to meet him for coffee."

XxXxXxX

The Doctor stood silently in the TARDIS ignoring everything around him. The fury building in his chest as the incident replayed in his mind. Whoever they were, these people had most certainly killed Clara. In most cases, he was willing to forestall judgement on intelligent beings. But that same courtesy did not extend to those who even touched his friends. In fact, now that they had done so, he would make absolutely certain that whatever this company was, it would never hurt anyone again. Even if he had to burn the building to the ground. And those that had killed her would most definitely face retribution. But first things first, he had to figure out what that place was and how to exploit their weakness.

Before he could make a move, the TARDIS phone rang. That sound had never been so welcome as it was now. For a brief moment, hope rose in his chest. If it was Clara, it meant she was alive. And if she was alive he still had a chance to save her. He leaned out of the door and answered the phone.

"Clara?" he called.

"Seven. Six. Five. One. Broadway." It was a computerized voice. Like different audio clips of people talking.

"Who is this?" he asked.

"Seven. Six. Five. One. Broadway." The voice repeated. Was that all it could say?

"What will I find there?" he asked.

"Help. Needed. Doctor." The voice said.

"I'll be right there," he replied.

He didn't know what the voice was. If it was going to help him, trap him, or anything. But right now he needed information. Even the smallest detail might help him save or avenge Clara. He launched himself into the TARDIS and fired it up. It landed with a thud a moment later.

Straightening his collar, he exited the TARDIS into a busy street. He didn't know what he was looking for so he kept his eye pealed for any anomalies.

"Excuse me," someone tapped on his arm. She was a head shorter than him and dressed in black. Even her fingernails were painted black. But the most obvious thing about her was the coy smile playing on her lips. Like she was holding in some great secret. "I'm supposed to take you for coffee."

XxXxXxX

End Notes: So I've already written out most of this story so I will be able to post it on a more regular basis. But for now, what do you think so far?

The author would like to thank you for your continued support. Your review has been posted.